Recombination, particularly viral recombination, can dramatically impact both evolution and epidemiology. In viruses, the recombination rate depends on the frequency at which co-infections occur and the frequency of genetic exchange between different viral genomes within an infected host cell. The ability to measure the recombination rate is important for understanding viral growth, virulence, and for creating attenuated strains for development of new vaccines.
Current methods for measuring the recombination rate, for example approaches involving gel electrophoresis and sequencing are either imprecise and/or time-consuming and often result in overestimation of the level of recombination. The methods, compositions, systems, and kits for recombination assays disclosed herein overcome many of these challenges. The methods, compositions, systems, and kits provided herein can also be used for other types of recombination analyses, such as bacterial recombination, recombination of V(D)J or VJ domains in immune cells, as well as other types of analyses such as haplotype analysis.